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Cryptic Diversity in Rodents from Costa Rica

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Cryptic Diversity in Rodents from Costa Rica Cryptic diversity in rodents from Costa Rica. Sara María Cáceres Valdés Master’s in Biodiversity, Genetics and Evolution Department of Biology 2018/2019 Supervisor Joana Maria Jorge Pereira de Castro Paupério, Postdoctoral Researcher, CIBIO-InBIO Co-supervisor Paulo Célio Pereira Martins Alves, Associate Professor, Faculty of Sciences, Univeristy of Porto, CIBIO-InBIO Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ FCUP i Cryptic diversity in rodents from Costa Rica Acknowledgements I would like to thank my wonderful supervisors for making this project being possible. A huge thanks to Paulo Célio, for welcome me in Portugal with open arms from the very beginning and for giving me the chance to be part of this interesting project where he co- supervised me and gave me a lot of support throughout the process. A very special thanks goes also to my supervisor Joana Paupério, for being so patient, for giving me great guidance and helping me when I needed the most. I feel so grateful to have worked with both. To the CTM laboratory team, Maria and Patrícia, a big thank for sharing their valued knowledge in the laboratory field, for all patience and help provided. And thanks to Sofía for not have ‘hanged’ me when an important sample flew out of the tube with alcohol because of me during my training. To my extraordinary classmates, thank you for all the meetings, typical meals, trips on the outskirts of Porto and all the good times we shared together, that made worth it to crossing over the Atlantic Ocean to spend this last 2 years. To Alexander Lépiz, for your valuable friendship in the short time we interact and to Sara Sampaio, for your kindness, support and availability to help me. A very emotional thanks to my beloved Panamanian friends, Darwin, Anette and Estibali, without whom this adventure would not have been so epic. Also, my dear Vítor and his wonderful family that make me feel at home and helped me feel a bit less homesick at times. My main and deepest thank goes to my MOTHER, without her support I would never have gotten where I am. Also, to my big sister Vlasty that together with mum form an important pillar of love and strength in my life (not forgetting our Benji). I also want to thank my father, for always supporting me as much as possible. I love you all Family! FCUP ii Cryptic diversity in rodents from Costa Rica Abstract Mesoamerica is one of the most important biodiversity hotspots, sheltering high levels of endemism and species diversity. This region holds about 6% of the World’s mammal diversity, of which, approximately 180 species are rodents. Within Mesoamerica, Costa Rica, is considered one of the 25 most biodiverse countries on the planet with the highest number of species per unit area. This country serves as corridor for diverse groups of mammals from the north to the south of the American continent. Therefore, the exchange of species between both regions, in addition to its topogeographical features, may have favoured crypic genetic diversity in some rodent groups as recent molecular studies and records of new species suggest. Considering the limited knownledge on the diversity of small mammals in Costa Rica and the importance of cryptic species for biodiversity conservation, this study aimed to analyse the spatial patterns of genetic variability in some rodent species, where high diversity was previously detected. Hence, 221 tissue samples from four genera of Cricetidae and one genus of Echimyidae were analysed. Of these, 15 were museum samples from the National Museum of Costa Rica and the Zoology Museum of the National University of Costa Rica. The genetic diversity was determined by amplifying two mitochondrial (cytb and COI) and two nuclear (IRBP and RAG1) genes. Our results show high genetic diversity in all the genera analysed, congruent with the geographic distribution of the species in Costa Rica. Some of the recognised lineages show deep divergence, and may even correspond to new cryptic species. This study describes cryptic diversity in small mammals from Costa Rica, highlighting the importance of this country for the conservation of biodiversity in Mesoamerica. FCUP iii Cryptic diversity in rodents from Costa Rica Keywords Small mammals, cryptic species, mitochondrial DNA, nuclear DNA, genetic diversity, Mesoamerica. FCUP iv Cryptic diversity in rodents from Costa Rica Resumo A Mesoamérica é uma das regiões do mundo com maior biodiversidade, albergando elevados níveis de endemismo e diversidade de espécies. Esta região detém cerca de 6% da diversidade de mamíferos ao nível mundial, incluindo aproximadamente 180 espécies de roedores. Dentro da Mesoamérica, a Costa Rica é considerada um dos 25 países com maior biodiversidade do planeta, com o maior número de espécies por unidade de área. Este país constitui um corredor para diversos grupos de mamíferos do norte ao sul do continente americano. Deste modo, o intercambio de espécies entre as duas regiões, assim como as suas características topogeográficas, pode ter favorecido a diversidade genética críptica em alguns grupos de roedores, como sugerem alguns estudos moleculares e descrições recentes de novas espécies. Considerando a escassez de conhecimento relativo à diversidade de pequenos mamíferos na Costa Rica e a importância da detecção de espécies crípticas para a conservação da biodiversidade, este estudo teve como objetivo principal o estudo dos padrões espaciais da variabilidade genética de alguns géneros das famílias Cricetidae e Echimyidae, nos quais tinha sido detectada recentemente elevada diversidade. Assim, neste estudo foram analisadas 221 amostras de tecido de quatro géneros de Cricetidae e de um género de Echimyidae. Destas, 15 eram do Museu Nacional da Costa Rica e do Museu de Zoologia da Universidade Nacional da Costa Rica. Foram amplificados e sequenciados dois genes mitocondriais (cytb e COI) e dois genes nucleares (IRBP e RAG1), com o objetivo de analisar a diversidade genética desses géneros na região. Os resultados obtidos permitiram detectar uma elevada diversidade genética em todos os géneros analisados, concordantes com a distribuição geográfica das espécies na Costa Rica. Algumas das linhagens identificadas apresentam uma elevada divergência podendo eventualmente corresponder a espécies crípticas. Este estudo descreve a ocorrência de diversidade críptica em pequenos mamíferos na Costa Rica, salientado a importância deste país para a preservação da biodiversidade na Mesoamérica. FCUP v Cryptic diversity in rodents from Costa Rica Palavras chave Pequenos mamíferos, espécies crípticas, ADN mitocondrial, ADN nuclear, diversidade genética, Mesoamérica. FCUP vi Cryptic diversity in rodents from Costa Rica Table of Contents Acknowledgements ............................................................................................................. i Abstract ................................................................................................................................ii Keywords ............................................................................................................................. iii Resumo................................................................................................................................iv Palavras chave .................................................................................................................... v Table of Contents ................................................................................................................vi List of Tables ...................................................................................................................... vii List of Figures ..................................................................................................................... x 1. Introduction .................................................................................................................. 1 1.1. Costa Rica, a biodiversity hotspot ....................................................................... 1 1.2. New World rodent cryptic speciation .................................................................. 3 1.2.1. Genus Oligoryzomys ..................................................................................... 5 1.2.2. Genus Nyctomys............................................................................................ 6 1.2.3. Genus Scotinomys ........................................................................................ 7 1.2.4. Genus Reithrodontomys ............................................................................... 8 1.2.5. Genus Proechimys ...................................................................................... 10 1.3. Molecular markers .............................................................................................. 11 1.4. Objectives............................................................................................................ 13 2. Material and Methods ................................................................................................ 14 2.1. Study area and sampling .................................................................................... 14 2.2. DNA extraction, amplification and sequencing ................................................ 15 2.2.1. Cytochrome b (cytb) .................................................................................... 15 2.2.2. Cytochrome c oxidase subunit I (COI) ......................................................
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